This is an updated analysis of Anderson et al. JAM manuscript "Rumen bacterial communities can be acclimated faster to high concentrate diets than currently implemented feedlot programs". The outputs generated through this analysis are identical to those of the original analysis. An updated analysis was conducted to mostly attempt better coding and reproducible research practices.

The R Markdown file in this repository contains the code for the analysis. Due to licensing issues, USEARCH can not be included in the setup to download automatically. To obtain a download link, go to the USEARCH download page and select version USEARCH v7.0.1090 for Mac OSX. The Fernando Lab has moved to vsearch for OTU picking, an open source alternative to USEARCH, but USEARCH is still implemented in the current analysis to reproduce the original work.

To start the analysis:

git clone https://github.com/chrisLanderson/2016_Anderson_et_al_JAM
cd 2016_Anderson_et_al_JAM
bash run.sh usearch_link

The analysis is setup to run in a Mac OS X environment, but can be easily switched to run in linux by uncommenting/commenting the appropriate lines in run.sh for Miniconda installation and downloaded a linux version of USEARCH.

A version of the rendered document is found in the repository - insert.